Introduction to Biology

[Byzesion]

Introduction to Biology
(GS201)

*Prerequisites*
None.

*Course Syllabus*
Before we start, please don't post in this thread. I'd like to keep it limited to the lectures for easier searching. Welcome, everyone. This is Introduction to Biology, and we will be covering three units (The Chemistry of Life, The Cell, and Genetics) over the course of ten weeks, with an eleventh week for the final.

There will be a test at the end of each unit, a mid-term in week five, and a final exam in week eleven. All of these are open-note.

Lectures are every Tuesday and Thursday, homework is issued at the end of the second weekly lecture, and is due by the next lecture. Late homework will be accepted, with a 5% penalty. If something wasn't clear, or you didn't understand something, or if you just need help, you can PM me anytime.

*Grading*
A - 100-85
B - 84-75
C - 74-65
D - 64-51
F - 50 or less

*Weight*
Homework - 50%
Tests - 10%
Mid-term - 15%
Final - 25%

As a special reward, the student with the highest grade in the class will receive :-X50.

*Cost*
This course is provided free of charge to any member of the 10000 Islands.

So if you want to sign up, please send me a PM. You can join up through week three with no questions asked, everything after that will be on a case-by-case basis.

[Byzesion]

I got absolutely no sleep from 10 AM Sunday to about 7 PM last night, so I'm going to keep this lecture kind of short.

There are certain recurring themes that connect the base concepts of the science of biology, and the core theme, the one idea that makes sense of what we know about life on Earth, is evolution. For instance, when you compare the Mongolian Velociraptor...



...with the domesticated chicken...



...there are noticeable similarities in shape and bone composition which shows, according to evolutionary biology, that becoming smaller and covered with feathers were advantageous to the species.

In addition, as complexity in the biological hierarchy increases, there are new or emergent properties that form as a result of the interactions and arrangement of the parts. For instance, if you place chlorophyll and all the other molecules that form chloroplasts, photosynthesis will not occur. All the molecules need to be properly arranged.

The basic activities of life, like movement, growth, reproduction, respiration, etc., are all types of work, and all work require energy. The transfer of energy between an organism and its surroundings usually requires a change in the form of energy. In photosynthesis, light energy causes a reaction between carbon dioxide and and water that creates sugars and oxygen.

Cells are the basis of all life on the planet. All organisms, from the smallest bacteria to the most complex plants and animals, are made entirely of cells. There are two main types of cells, Prokaryotic, which are usually single-celled organisms like bacteria, and Eukaryotic, which are usually part of a larger organism.

Of the 92 naturally occurring elements, about 25 are known to be essential to life, and just four make up 96% of living matter - Carbon, Oxygen, Hydrogen, and Nitrogen. Another seven make up most of the remaining 4% - Calcium, Phosphorus, Potassium, Sulfur, Sodium, Chlorine, and Magnesium. Some of the remaining trace elements are necessary for all forms of life, such as Iron. Others are only needed by certain species. For instance, in vertebrates, Iodine is an essential ingredient of a hormone produced by the thyroid gland. Without it, the thyroid grows to an abnormal size, a condition known as a goiter.

[Byzesion]

Water on Earth is so common, that it's easy to overlook its extraordinary qualities. When studied in isolation, the water molecule is deceptively simple. It's shaped something like a wide V, with the two hydrogen atoms bonded to the oxygen, and it is this uneven distribution of electrons that makes it a polar molecule, meaning that the hydrogen end has a slight positive charge, and the oxygen a slight negative one.

The overall result of this polar nature is that molecules of water will form a weak magnetic attraction to each other. In its liquid form, these hydrogen bonds are very fragile, forming, breaking, and re-forming in only a few trillionths of a second. Because of this, liquid water is more structured than most other liquids, which is why hitting water at a high speed is just as dangerous as hitting a wall.

All the various hydrogen bonds work in concert to hold the water together, a phenomenon known as cohesion. This cohesion, combined with adhesion (the clinging of one substance to another) makes it possible for plants to absorb water from their roots to the top of the tallest trees. Related to this is the concept of surface tension, a measure of how difficult it is to break or stretch the surface of a liquid. This property of water is why some animals can stand and move on water.

Despite popular claims, water is not a universal solvent. If it were, there would be no life on Earth. However, it is a very versatile solvent, a result of its polar nature. For instance, imagine a spoonful of salt is dissolved in a glass of water. When the salt comes in contact with water, the oxygen end is attracted to the positively charged sodium atoms, and the hydrogen end is attracted to the negatively charged chlorine atoms. Water molecules surround the individual ions, separating them and shielding them from one another. This shield is known as a hydration shell.

*Homework*
1. What is the basis of modern biology?
2. As biological complexity increases, new properties arise from the ______ and ______ of chemicals.
3. How does photosynthesis work?
4.What type of cells make up multi-cellular organisms?
5.Which four elements are most essential to life?
6.What kind of molecule is water?
7.How does liquid water stay together?
8.How is water transfered up the trunks of trees?
9.How does water dissolve molecules?

[Anartonia]

Homework 1:

(1.)The basis of biology is evolution: the theory that species evolve from other species by gaining and/or losing traits.
(2.)"As biological complexity increases, new properties arise from the interactions and arrangement of chemicals."
(3.) The process of photosynthesis occurs when the energy from light (sunlight) is used to make a reaction between carbon dioxide and water. The end products are sugar (glucose) and oxygen.
(4.) Eukaryotic cells mostly make up multicellular organisms. (Prokaryotic cells are mostly unicellular organisms.)
(5.) The 4 most vital elements to life are hydrogen, carbon, nitrogen, and oxygen.
(6.) Water is a polar molecule; it is similar to a magnet because the oxygen atom on one side of the molecule is negatively charged, while the two hydrogen atoms on the other side are positively charged.
(7.) The hydrogen bonds in the water molecules hold the molecules together via cohesion.
(8.) Water can travel through tree trunks as a result of the water molecules' cohesion combined with adhesion, which is when one substance attaches to another.
(9.) Due to water being a polar molecule, it dissolves many substances very easily. When a certain substance is dissolved in water, the water molecules use their polarity to adhere to and separate the charged atoms, or ions, in the molecules of the other substance. This dissolves the substance.

[Byzesion]

Okay, well...we're off to a late start tonight. Since the next chapter deals with proteins and other larger molecules, it's best to focus a little bit on carbon. Or more specifically, on the way that the versatile nature of carbon allows it to form the backbone of the molecules of life.

Back in the early 1800s, it was a commonly held belief among chemists that the compounds found in living organisms were far to complex to be synthesized. It was all part of the whole vitalism doctrine, related to the medical idea of humors and herbal remedies. So, the vast majority chemists called these difficult compounds "organic", and immediately went back to studying less challenging fare. But a hardy few, like Friedrich Wöhler and William Henry Perkin, decided to investigate these compounds, moves that resulted in the synthesis of urea from ammonium cyanate (NH₄CNO) and the organic dye Perkin's Mauve.

Carbon has six electrons, with two in the lowest level and four in the highest level, which gives it a valence of four, meaning that it takes four electrons to complete the upper level. This tetravalence is what makes carbon so versatile. It can create four covalent bonds, like in methane, two double bonds, like in carbon dioxide, or one double and two single bonds, like ethylene.

fig 1.


All of these molecules are hydrocarbons, molecules consisting of entirely of hydrogen and carbon. These hydrocarbons are the main component of petroleum, made of partially decomposed plants and animals from millions of years ago. Most hydrocarbons are not present in living beings, even though there are many molecules that have hydrocarbons in them, such as fats in animals, which have long hydrocarbon tails attached to non-hydrocarbon molecules.

Most of the hydrocarbon molecules are hydrophobic, meaning they repel water, mainly due to the fact that the bonds are relatively nonpolar carbon-to-hydrogen bonds. This is in addition to their ability to store and release energy when exposed to proper conditions, examples being the violent reaction gasoline undergoes exposed to heat and oxygen, or body fat serving as stored fuel for animals.

Now, a variation in the structure of a molecule results in an isomer. There are three major types of isomers: Structural isomers, which differ in arrangements of the atoms like propanol (oxygen-hydrogen bond at the end) and isopropyl alcohol (oxygen-hydrogen bond in the middle); Geometric isomers, where the links are in the same place, but the atoms themselves may not be; and Enantiomers, which are simple mirror images of a molecule.

Well, I'm going to wrap this up because it's getting late. Next week are life-essential molecules and proteins.

[Byzesion]

Last lecture I mentioned that in addition to proteins, we would be covering examples of life-essential molecules. Out of all the organic chemical groups involved in the processes of life, there are about six that are the most reactive and functional.

• The Hydroxyl group, which has a hydrogen atom bonded to an oxygen, which is then bonded to a hydrocarbon backbone. Hydroxyl compounds are known as alcohols. Examples include ethanol, commonly known as grain alcohol, and isopropyl, or rubbing alcohol.
  
• The Carbonyl group, consisting of an oxygen atom double-bonded to part of the hydrocarbon backbone. Its compounds are known as ketones if it is within the backbone, or aldehydes if it comes at the end. An example of a ketone is acetone, used as a paint thinner, and an example of an aldehyde is formaldehyde, used to preserve the deceased.
  
• The Carboxyl group, formed by a carbonyl group bonded to a hydroxyl. It creates compounds known as carboxylic, or organic, acids, and a common example is acetic acid, which gives vinegar its bite.
  
• The Amino group, made up of nitrogen bonded with two hydrogen atoms. It creates amines, such as the disinfectant ammonia, or phenylalanine, which is used in artificial sweeteners. Since phenylalanine contains both an amino and a carboxyl, it's known as an amino acid.
  
• The Sulfhydryl group, which is sulfur bonded with a hydrogen atom, creating compounds known as thiols. Well known thiols are methanethiol or methyl mercaptan, which is a component of flatus, or ethanethiol, which is added to natural gas to aid in leak detection.
  
• The Phosphate group, a phosphorus atom bonded to four oxygens, one of which is bonded to the hydrocarbon backbone. Compounds with phosphate groups in them are simply known as phosphates. An example is glycerol phosphate, which creates enzymes in the bones and muscles of animals, or adenosine triphosphate, which transports energy in cells for the process of metabolism.
  

In addition, a seventh group, the Methyl group (carbon bonded with three hydrogens), acts as a tag for biological molecules.

The critically important large molecules of all life on Earth - from single-celled bacteria to blue whales - fall into just four categories: Carbohydrates, Lipids, Proteins, and Nucleic Acids. Of these, all except lipids are known as macromolecules. Macromolecules are long polymers, strings of similar or identical building blocks, or monomers.

These classes of polymers differ in the composition of their monomers, but the chemical process by which they are created and broken are constant. When a monomer connects to another monomer or a polymer, a molecule of water is created by a reaction between a hydrogen atom and a hydroxyl. This water is then expelled from the newly-minted polymer, and the ends linked together. Similarly, polymers are broken down into their constituent components when a water molecule is added in, breaking down into a hydroxyl and an atom of hydrogen, which are absorbed by the shorter polymer and the monomer.

Carbohydrates serve as fuel for life and as building materials. All of the carbohydrates can be broken down into a few classes: Monosaccharides, or simple sugars, which include glucose, sucrose, and fructose; Disaccharides, which are short polymers made of two simple sugars; Storage Polysaccharides, longer polymers which make up starch in plants and glycogen in animals; and Structural Polysaccharides, extremely long chains of glucose making up cellulose, a major component of plant cell walls.

Lipids are compounds grouped together through a shared hydrophobia, or an intense aversion to water. Lipids can be broken down into saturated fats, which remain solid at room temperature, unsaturated fats, which are liquid at room temperature, phospholipids, which create animal cell membranes, and steroids, such as cholesterol, which is synthesized into hormones.

Proteins are by far the most important polymers to life, making up more than half of the dry weight of cells. Proteins can be broken down into the following eight categories.

• Enzymatic Proteins, proteins which selectively accelerate chemical reactions without being consumed by them, such as converting complex sugars to simple ones.
  
• Structural Proteins, proteins that form structural support tissues, such as collagen in connective tissues and keratin in hair and fingernails.
  
• Storage Proteins, proteins that store amino acids for future consumption, such as ovalbumin in egg whites or caesin in milk.
  
• Transport Proteins, which transport substances to other tissues in the body, such as hemoglobin transporting oxygen in the blood.
  
• Hormonal Proteins, proteins that regulate and coordinate an organism's activities, such as insulin regulating the amount of sugar in blood.
  
• Receptor Proteins, proteins that respond to chemical stimulus of a cell, such as receptors in nerve cells that respond to chemicals released by other nerve cells.
  
• Contractile and Motor Proteins, proteins responsible for movement, such as actin and myosin, which are responsible muscle contractions.
  
• Defensive Proteins, which protect against disease, such as antibodies combating bacterial and viral infections.
  
  Okay, that's all for this lecture. Homework and unit 1 test will be posted tomorrow. Next week, we start on the cell as a whole.
  

[Byzesion]

Homework (week 3 & 4)
1. What does the term "organic" stem from?
2. Who is responsible for synthesizing urea from ammonium cyanate?
3. How many electrons does the lowest level hold?
4. Why do hydrocarbons repel water?
5. Describe structural isomers.
6. What are the six most reactive chemical groups?
7. Starches are what type of carbohydrates?
8. What type of lipid is vegetable oil?
9. What is the function of enzymatic proteins?

Test (Unit 1)
1. What is the fuel created during photosynthesis?
2. How many elements are essential to life?
3. What happens to vertebrates in the absence of dietary iodine?
4. How is it possible for plants to pull water up from their roots to their leaves?
5. What is a solvent?
6. What is valence?
7. What is the molecular formula of methane?
8. What is the difference between propanol and isopropyl alcohol?
9. What is the use of ethanethiol?
10. What is the function of the methanol group?
11. What is keratin and what does it form in animals?
12. Low blood sugar is caused by an excess of what type of protein?

[Byzesion]

Before we get into the subject of cells, we have to cover how cells are studied. Before about 1590, it was completely impossible to study cells smaller than about 200 micrometers. Until then, there wasn't a device capable of that level of magnification. And even then the microscope wasn't used to it's full potential; it would take a little more than fifty years until anyone decided to look at living tissue, in Giambattista Odierna's The Fly's Eye. But micrography really took off starting in the 1660s and 1670s, when the microscope began to see extensive use in England, Italy, and the Netherlands as a research tool, partly due to Robert Hooke's Micrographia and its impressive illustrations. The greatest contributions, however, came from Dutch scientist Antonie van Leeuwenhoek, who discovered red blood cells, spermatozoa, and was the first to report of micro-organisms.

These first microscopes, and indeed most of the more common microscopes today, were light microscopes - microscopes that pass light through the specimen, and then through the glass lens or lenses, which refracts the light in such a way as to make the specimen appear much larger than it actually is. These types of microscopes are commonly found in elementary, middle, and high school classrooms.

However, research grade microscopy today relies on electron microscopes, which depending on quality and method of measurement, can see specimens on the atomic scale.

In addition to microscopy, another process useful in identifying the cellular components and their functions is cell fractionation. In cell fractionation, tissues are homogenized in a blender, then spun in a centrifuge to filter out increasingly fine particles.

That's all for tonight. Part two of this chapter will go up tomorrow.

[Byzesion]

Continuing from last night, we are going to go over the look and function of the various cellular parts. First, the prokaryotic cell.



In a prokaryotic cell, the genetic information, encoded in long strands of DNA, are present in the form of an unbound nucleoid in the center.





While in plant and animal eukaryotic cells, the DNA is contained in a membrane-bound nucleus. In both cell types, the DNA instructs the ribosomes to synthesize proteins by releasing messenger RNA, which is read by the ribosomes by way of being passed between the two sub-units, much in the same way that a VCR or tape player reads the information on magnetic tape. Many of these ribosomes are located in the endoplasmic reticulum, a large membrane system surrounding the nucleus.

This membrane system is made up of two distinct yet connected systems: the rough endoplasmic reticulum and the smooth endoplasmic reticulum. The smooth ER contains enzymes responsible for synthesis of steroid hormones, such as adrenaline in the adrenal glands or testosterone and estrogen in the reproductive organs. Others are responsible for the detoxification of drugs or alcohol, usually by adding hydroxyl groups making the substances easier to flush from the body.

The rough ER, on the other hand, is responsible for the production of proteins within a cell, such as producing insulin in the pancreas or digestive enzymes in the stomach.

That will wrap it up for today. Tomorrow, the rest of the cell and more of their functions.

[Anartonia]

Homework | Weeks 3 & 4 (with a one-day extension):

(1.) "Organic" stems from the word "organism". It was coined by chemists in the early 1800s who believed that the natural compounds in living organisms were too complicated to understand.
(2.) Chemists such as Friedrich Wöhler and William Henry Perkin who decided to explore the field of "organic" compounds synthesized urea from ammonium cyanate.
(3.) The lowest level of an atom can hold up to 2 electrons.
(4.) Hydrocarbons repel water because they are generally nonpolar and therefore are not attracted to polar water molecules.
(5.) A structural isomer is a variation in the arrangement of the atoms in a molecule.
(6.) The six most reactive chemical groups are the Hydroxyl group (alcohols), the Carbonyl group (ketones and aldehydes), the Carboxyl group (carboxylic acids), the Amino group (amines), the Sulfhydryl group (thiols), and the Phosphate group (phosphates). A 7^th group, the Methyl group, is a "tag" for biological molecules.
(7.) Starches are Storage Polysaccharides, which are complex carbohydrates and long macromolecules.
(8.) Vegetable is an unsaturated fat. It is a liquid at room temperature.
(9.) Enzymatic Proteins (or enzymes) speed up certain chemical reactions without becoming part of them. Different Enzymatic Proteins accelerate different reactions.

[Anartonia]

Sorry for the late test; had RL preoccupations

(1.) During photosynthesis, water and carbon dioxide are converted to sugar (glucose) and oxygen. The glucose is the energy the plant needs to survive.
(2.) About 25 elements are essential for life.
(3.) If vertebrates are deprived of dietary iodine, which is in a hormone produced by the thyroid gland, the thyroid will grow to an unusually large size. This is called goiter.
(4.) Hydrogen atoms in water molecules hold the molecule together, which is called cohesion. Plants can pull up water via their roots when cohesion is combined with adhesion,, or the ability to stick to another substance,
(5.) A solvent is a liquid that dissolves another substance.
(6.) The valence of an atom is the number of electrons needed to complete the uppermost level where there are already electrons.
(7.) The molecular formula for methane is CH₄; four hydrogen atoms attached to a carbon atom.
(8.) Propanol and isopropyl alcohol are structural isomers, meaning that they have different molecular structures.
(9.) Ethanethiol, which is in the sulfhydryl group, is added to natural gas to make leaks more noticeable.
(10.) By "methanol", did you mean "methyl"? I couldn't find anything in the previously posted homework about a methanol group. The methyl group functions as a tag for biological molecules.
(11.) Keratin is a structural protein, and it is found in hair and nails.
(12.) Low blood sugar is caused by excess hormonal proteins; too much insulin in the bloodstream will reduce the amount of sugar in the blood.